Figshare+
Browse
.ZIP
admin_esther_110723-Cell1.zip (17.41 GB)
.ZIP
kinetic_sig_control_43_model.zip (15.95 GB)
.ZIP
kinetic_sig_control_model.zip (16.57 GB)
1/0
3 files

SMRT-seq for m6A methylation analysis dataset for Pseudomonas aeruginosa PAO1 37°C vs. 43°C

dataset
posted on 2024-10-18, 22:17 authored by Esther ShmidovEsther Shmidov, Alexis Villani, Joseph Bondy-Denomy, Ehud Banin

The data in this item includes Single-molecule real-time sequencing (SMRT-seq) data generated using PacBio Sequel I for high-resolution analysis of m6A methylation from post-43°C grown bacteria and during the recovery period.

Sample preparation: Overall, 15 samples included 3 replicates of Pseudomonas aeruginosa after exposure to 37 °C (control) or 43 °C at 4 time points (T = 0 generations, T = 5 generations, T = 22 generations, and T = 54 generations). Samples from the T=0 groups are simply labeled “37” or “43”.

Analysis: Pac Bio subreads were mapped to the reference genome Pseudomonas aeruginosa PAO1 GCA000006765, ASM676v1, for each sample separately, using the pbmm2 tool from the smrttools 10 toolkit (Pac Bio). m6A modifications were then inferred with the ipdSummary tools. The control model was used in two separate runs. In the first run samples from the group 43 were used as reference. In the second run, samples from the group 37 were used as reference. Sites with ipd-ratio with p-value < 0.05 were considered to have a new modification in the sample, compared with the reference. Each sample was tested with the reference of the same line, e.g. 1_43_5g was tested against 1_43 or 1_37. 2_43_22g was tested against 2_43 or 2_37, and so on.

History

Research Institution(s)

Bar-Ilan University, UCSF

I confirm there is no human personally identifiable information in the files or description shared

  • Yes

I confirm the files and description shared may be publicly distributed under the license selected

  • Yes

Usage metrics

    Figshare+

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC